If you are trying to work up reactions with boronic acids, you might want to try the following:
Note: I made the assumption that your products will probably be soluble in EtOAc
Filter out the junk in a simple filter packed with celite and remove MeOH by rotovap. Then try working up the crude in 0.1M NaOH, Na2CO3 or similar base. This objective is to break up the boron crosslinking with the amines and the alcohols to free up your target product. Check to see if your target is in the organic phase (EtOAc), if it is, then you are probably in good shape.
Filter out the junk in a simple filter packed with celite and remove MeOH by rotovap. Place crude in dH20 and very very slowly add strong acid (HCl) to precipitate boronic acids since most boronic acids are not readily soluble in water. Once you get the precipitate, you might want to work up the aqueous solution since the protonated amine in your target may be enough to get it dissolve in water.
Hope these small tips will help.